Biology Commons^™

Uncovering The Mechanism Of Reep2-Mediated Emt-Driven Membrane Trafficking In Lung Adenocarcinoma, Kevin Fulp

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking is frequently disrupted during cancer progression, and the underlying mechanisms remain largely unknown. Currently, no effective drugs target dysregulated membrane trafficking for cancer treatment. Recent evidence has demonstrated that epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma (LUAD) employs a membrane trafficking program to coordinate cancer cell invasion and immunosuppression. To further dissect the pro-tumorigenic membrane trafficking program, we initiated an in vivo CRISPRi screen to assess more than 2,000 membrane trafficking-related genes in a syngeneic mouse LUAD model. We identified REEP2, an endoplasmic reticulum (ER) shaping protein, as a novel regulator of EMT-driven membrane trafficking. High REEP2 expression is …

Reep2-Driven Pro-Metastatic Secretion Promotes Lung Cancer Progression, Oluwafunminiyi E. Obaleye

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking plays a critical role in cellular function and is frequently dysregulated in cancer to promote metastasis. In lung adenocarcinoma (LUAD), the epithelial-to-mesenchymal transition (EMT) activating transcription factor, ZEB1, drives a pro-metastatic membrane trafficking program; however, the underlying molecular mechanisms remain poorly understood. Using a CRISPR interference (CRISPRi) in vivo screen of 2,099 membrane trafficking regulators in a syngeneic mouse model of EMT-driven LUAD, we identified REEP2 — an endoplasmic reticulum (ER) shaping protein — as a critical regulator of tumor progression. REEP2 mRNA expression correlates with poor prognosis, EMT signatures, and an immunosuppressive tumor microenvironment in LUAD patients. …

Do Magnesium Ions Have Similar Effects As Calcium Ions On Resting Membrane Potential?, Anthony Hana, Youngwoo Kim, Joy Bidros, Katie Neglia, Robin L. Cooper

Biology Faculty Publications

Maintaining a membrane electrical potential of biological cells is a dynamic process, as some cells have a continually changing potential, like pacemaker cells, while other cells may function with large or small changes in the membrane potential. Additionally, some cells may change their electrical potential when stimulated or inhibited by electrical signals, chemical compounds, or both—either simultaneously or episodically. The persistent leak of K⁺ through two-pore-domain potassium channels (K2P) and of Na⁺ through Na⁺ leak channels (NALCNs) and the action of pumps and exchangers are primarily responsible for maintaining a resting potential. Ca²⁺ ions are known …

An Evolving View Of Lineage Diversification, Pascal O. Title, L. Francisco Henao-Díaz, Rosana Zenil-Ferguson, Thais Vasconcelos

Biology Faculty Publications

Systematists have long been fascinated by the astounding variation in species diversity across the various branches of the tree of life, a net result of the uneven rates at which lineages undergo speciation and extinction over time. The past 30 years have seen the development and widespread application of tools that allow diversification to be quantified and characterized in empirical data sets. These advances have, in turn, enabled the statistical evaluation of hypotheses about the causes behind the uneven distribution of species richness among lineages, leading to a more nuanced understanding of diversification rate variation, as reflected in an ever-expanding …

Exogenous Estradiol Does Not Regulate Daily Metabolic Rhythms Underlying Diet-Induced Obesity In Male Mice, W. Brad Osborne, Oliver Vöcking, Victoria Alvord, Oluwabukola Omotola, Yuriko Katsumata, Julie S. Pendergast

Biology Faculty Publications

Male mice fed high-fat diet become obese, but female mice are resistant to diet-induced weight gain. We previously found that circulating estradiol in females protects their daily rhythms from disruption by high-fat feeding to prevent diet-induced obesity. The goal of this study was to determine the effects of estradiol on daily metabolic rhythms in male mice. Male C57BL/6J mice were treated with estradiol and fed high-fat diet for 2 weeks. We measured the effects of high-fat diet feeding on daily rhythms of eating behavior and locomotor activity, and on the phases, or timing, of circadian rhythms in central and peripheral …

Drinking Microstructure Analysis Of Direct Controls Of Water Intake In Male And Female Rats, Bo W. Sortman, Emalie L. Mullane, Kennedy L. Lamb, Andrea A. Edwards, Ann-Marie Torregrossa, Derek Daniels, Jessica Santollo

Biology Faculty Publications

Measures of rodent drinking (lick) patterns are used to test how various manipulations affect fluid intake. Decades of research indicate that manipulating the satiating potency of a stimulus affects the number of licking bursts whereas manipulating the hedonic value of the solution affects the size of the licking bursts or rate of licking. This type of analysis has been largely applied to manipulations that modulate drinking that is already occurring (i.e., indirect controls or modulators of intake), but there is a dearth of studies with detailed measures of licking due to stimuli that are primary drivers of intake which happen …

Using Camera-Based Unmarked Spatial Capture-Recapture Modeling To Estimate Reintroduced Elk (Cervus Canadensis) Population Parameters And Distribution In Southeastern Kentucky, Claire Marie Muia

Theses and Dissertations--Forestry and Natural Resources

Estimation of population parameters is important for wildlife management decisions. Elk reintroduced to southeastern Kentucky experienced early irruptive population growth and are currently monitored using a statewide harvest-based statistical population reconstruction model (SPR) across the Kentucky Elk Restoration Zone (KERZ). Because the SPR model is spatially coarse and difficult to scale to the smaller management units comprising the KERZ, we conducted a spatially explicit capture-recapture study using a clustered camera-trapping array deployed for 10 weeks from June–August 2024 to estimate elk population parameters within Management Unit 4. Due to a lack of resights of GPS-marked elk, population parameters were estimated …

Modeling Inherited Retinal Disease In Zebrafish, Meet Patel

Theses and Dissertations--Biology

Inherited retinal diseases (IRDs) affect millions of people worldwide. Majority of IRDs are caused by degeneration of rod and cone photoreceptor cells (PRCs) due to gene mutations. The overarching goal of my dissertation is to model and evaluate the molecular role of various gene candidates involved in IRDs such as cone rod dystrophy (CRD) and retinitis pigmentosa (RP).

Mutations in CDHR1, a photoreceptor specific cadherin have been associated with CRD and recapitulated in mouse CDHR1 knockouts. However, the molecular function of CDHR1 remains unknown. CDHR1 has been shown to localize at the leading edge of murine rod nascent outer segment …

Chromatin Remodeling Protein Bptf Mediates Chromatin Accessibility At Gene Promoters In Planarian Stem Cells, Prince Verma, John M. Allen, Alejandro Sánchez Alvarado, Elizabeth M. Duncan

Biology Faculty Publications

Background The regulation of chromatin accessibility is essential in eukaryotic cells as one of several mechanisms that ensure gene activation occurs at appropriate times and in appropriate cell types. Accordingly, mutations in chromatin remodeling proteins are linked to many different developmental disorders and cancers. One example of a chromatin protein that has been linked to both developmental abnormalities and cancer is BPTF/NURF301, the largest subunit of the Nucleosome Remodeling Factor (NuRF) complex. The BPTF subunit is not only important for the formation of NuRF but also helps direct its activity to particular regions of chromatin by preferentially binding histone H3 …

A Framework For Modeling The Impacts Of Adaptive Search Intensity On The Efficiency Of Abundance Surveys., Laura Jiménez, John R Fieberg, Michael Mccartney, Jake M Ferguson

Biology Faculty Publications

When planning abundance surveys, the impact of search intensity on the quality of the density estimates is rarely considered. We constructed a time-budget modeling framework for abundance surveys using principles from optimal foraging theory. We link search intensity to the number of sample units surveyed, searcher detection probability, the number of detections made, and the precision of the estimated population density. This framework allowed us to determine how a searcher should behave to produce optimized density estimates. Using data collected from quadrat and removal surveys of zebra mussels (Dreissena polymorpha) in central Minnesota, we applied this framework to evaluate potential …

Feeding Systems And Fresh Lamb Color Stability, Koushik Mondal

Theses and Dissertations--Animal and Food Sciences

Consumers consider the surface color of fresh lamb as the indicator of freshness and wholesomeness, which affects their purchase decisions. The redox chemistry of myoglobin (Mb) determines the color of fresh lamb. Artificial raising on milk replacer (a pre-weaning strategy) as well as red clover supplementation are management strategies used in lamb production. This thesis focuses on the effects of artificial raising on milk replacer and red clover supplementation on the color and oxidative stability of fresh lamb.

In the first experiment, the effect of pre-weaning with milk replacer on the carcass attributes, color stability and lipid oxidation of lamb …

Considerations And Applications Of Environmental Dna In Biodiversity Studies, Sarah Tomke

Theses and Dissertations--Forestry and Natural Resources

Environmental DNA (eDNA) sampling—the detection of species through genetic material shed into the environment—has become an efficient and reliable method for biodiversity assessments. The method has grown in popularity due to its non-invasive and non-destructive nature, and has revolutionized monitoring efforts for rare, elusive, and cryptic species for which traditional sampling approaches are often costly and ineffective. Hundreds of studies have utilized this technique to study species occupancy, delineate distributions, and assess relative community composition. Although eDNA sampling is an effective strategy for many conservation and ecological studies, recently, light has been shed on some of its potential drawbacks and …

Effects Of Neonatal Estradiol Treatment On Regulating Sexual Differentiation Of Daily Rhythms Underlying Diet-Induced Obesity In Female Mice, Samuel Nwadialo

Theses and Dissertations--Biology

Sex differences of the brain and behavior often require the combination of organizational and activational effects of sex hormones. The activational effects of estrogens in adult female mice protect daily eating and activity rhythms from disruption by high-fat diet feeding and inhibit diet-induced obesity. However, male mice have disrupted eating rhythms when fed high-fat diet and this causes obesity. Treatment of adult male mice with estradiol does not protect rhythms from disruption by high-fat diet, as it does in females. In this study, we sought to determine whether the organizational effects of estradiol masculinize the daily eating and activity rhythms …

Investigations Across Biology And Education: Exploring The Gut Microbiome Of Freshwater Mussels And Understanding Undergraduate Biology Student Motivation, Mary Foley

Theses and Dissertations--Biology

A PhD aims to make a unique contribution to the current body of knowledge while developing as an independent researcher and critical thinker. This dissertation covers a wide range of topics, from microbiome analysis to biology education. Although there is no broad overarching research theme, all the chapters are connected by the process of scientific inquiry and by their contribution to the completion of a PhD.

Chapter One serves as a comprehensive literature review, delving into the standard methods of measuring the health of at-risk species. It describes direct measures of health (e.g., birth and death rates) crucial for predicting …

Estrogen Signaling Regulates The Sex Difference In Resynchronization To Abrupt Shifts Of The Light-Dark Cycle In A Mouse Model Of Jet Lag, Maria Venegas

Theses and Dissertations--Biology

The circadian system coordinates 24-hour cycles of internal biological processes with the environmental light-dark cycle. Abrupt shifts in the timing of the light-dark cycle misalign internal circadian clocks with the environment and cause jet lag until resynchronization occurs. The objective of this study was to investigate the mechanisms underlying sex differences in jet lag in mice. Female mice resynchronized faster than male mice to 6-hour advances and delays of the light-dark cycle, which mimicked eastward and westward travel, respectively. Circulating estradiol was necessary for rapid resynchronization in female mice since ovariectomized females resynchronized slower than mice treated with estradiol. We …

All Eyes On The Spiny Mouse: An Investigation Into Acomys Dimidiatus As A Model For Retinal Biology And Regeneration, Jessica D. Bills

Theses and Dissertations--Biology

The retina is a complex tissue with six types of neurons, supported by an intrinsic glia cell, that work in concert to input a visual stimulus and relay a visual message to the brain. Efficient communication between neurons is vital to this process and each neuron plays a significant role in vision. When retinal neurons degenerate, that visual signal is lost. Degenerative eye diseases affect the neurons of the retina in millions of people world-wide and can ultimately lead to blindness. While treatments are evolving, most are designed to prevent further damage; the field has yet to piece together how …

Assessing Endophyte Frequency Distributions And The Effect Of Epichloë Brachyelytri In The Chemotypic And Genotypic Diversity Of Brachyelytrum Erectum, Rachel Ann Sneed

Theses and Dissertations--Plant Pathology

Seed-transmissible epichloid fungal endophytes are best known for their roles as defensive mutualists in cool-season grasses. Historically, the discovery of fungal endophytes was driven by investigations of plant toxicity to livestock, followed by extensive study of their alkaloids and protection against insects and nematodes. Epichloae can produce four classes of alkaloids: ergot alkaloids, lolines (saturated aminopyrrolizidines), indole–diterpenes, and peramine. It is increasingly evident that these hereditary symbionts have much more diverse chemical profiles both in individual populations and between them. To this end, differences in chemotypic profiles of these symbionts may translate to different evolutionary and environmental advantages across plant …

Transient Interactions Modulate The Affinity Of Nf-Κb Transcription Factors For Dna, Tianjie Li, Shandy Shahabi, Tapan Biswas, Oleg V. Tsodikov, Wenfei Pan, De-Bin Huang, Vivien Ya-Fan Wang, Yi Wang, Gourisankar Ghosh

Biology Faculty Publications

The dimeric nuclear factor kappa B (NF- κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10- fold higher than with G or C. The crystal structures of neither the complexes nor …

Eliciting The Effect Free Roaming Cats Have On Native Hawaiian Wildlife Using Stable Isotope Analysis, Erin Salano

Theses and Dissertations--Biology

This study measured the concentration of the stable isotopes Carbon and Nitrogen within the tissues of free-roaming and indoor cats on the Hawai’ian islands. This study aimed to determine whether cats are consuming more human provisioned or wild food sources and whether their diet is having a negative impact on endemic species; with a focus on assessing impacts on conserved bird populations. We hypothesized that human provisioned food sources have higher levels of carbon due to the amount of corn fillers within them, while wild food sources are more Nitrogen rich. We found that indoor and feral cats sampled from …

Data For "Linking Previous Experiences To Behavior And Health In The Honey Bee (Apis Mellifera)"", Rebecca R. Westwick, Clare C. Rittschof, Gavin P. Brackett, Cameron E. Brown, Bethany J. Ison, Zainulabbeudin Syed, Anna M. Foose

Entomology Research Data

An organism’s ability to respond to changing conditions can be vital to its success. Indeed, plasticity is a common feature of living organisms. Much of the research in this area, though, has focused on effects caused by environmental conditions. What has received relatively less attention is how social experiences and broader features of an organism’s social environment can lead to long-lasting changes in health and behavior. This knowledge gap exists despite the well-documented existence of health and behavioral effects after social interactions in certain taxa such as humans.

Social insects such as honey bees provide an excellent opportunity to better …

Effects Of Translocation On Eastern Black-Tailed Rattlesnakes (Crotalus Ornatus) In The Northern Chihuahuan Desert, Jacob A. Coffman

Lewis Honors College Thesis Collection

AS HUMANITY continues to grow and expand, we inevitably encroach on wildlife habitat. This can create conflict between humans and wildlife. Human wildlife conflict usually occurs when humans are near areas where wildlife typically reside. A prime example is a farmer coming into conflict with animals that predate their seeds or livestock. The most common response to this problem in many areas is lethal control to prevent economic loss (Dickman 2010). This seems like an immediate resolution of the conflict in the human’s perspective, but this action can have many adverse effects. This killing may result in negative social outcry, …

Linking Previous Experiences To Behavior And Health In The Honey Bee (Apis Mellifera), Rebecca R. Westwick

Theses and Dissertations--Entomology

An organism’s ability to respond to changing conditions can be vital to its success. Indeed, plasticity is a common feature of living organisms. Much of the research in this area, though, has focused on effects caused by environmental conditions. What has received relatively less attention is how social experiences and broader features of an organism’s social environment can lead to long-lasting changes in health and behavior. This knowledge gap exists despite the well-documented existence of health and behavioral effects after social interactions in certain taxa such as humans.

Social insects such as honey bees provide an excellent opportunity to better …

Exploring The Molecular Basis Of Touch: A Comparative Analysis Of Gene Expression In Sensory Corpuscle-Rich And Corpuscle-Poor Skin Regions In The Duck, Thomas Hart

Theses and Dissertations--Biology

Cutaneous touch is facilitated by discrete cellular complexes composed of non-neuronal cells associated with mechanoreceptor neuron endings. The non-neuronal cells of these cutaneous end organ complexes (CEOCs) are believed to contribute to touch, but their role in touch sensation remains unclear. To better understand the function of CEOC cells, we sought to characterize the transcriptional profile of CEOC-rich tissue and identify genes expressed in CEOC cells. Bill skin of the tactile foraging Pekin duck (Anas platyrhynchos) is dense with CEOCs, specifically the avian analogs of mammalian Pacinian and Meissner corpuscles, while corpuscles in duck foot skin are scarce. Using RNA …

Variation In Behavioral Strategies For Coping With Environmental Uncertainty, Allison Mclaughlin

Theses and Dissertations--Biology

My dissertation investigates how animals behaviorally respond to environmental change, especially when there is limited information about that change. Uncertainty about the environment comes in various forms, including food resources which vary unpredictably and novel cues which present an unknown level of potential risk or benefit. Various behavioral strategies help animals cope with such uncertainty. Tactics to manage unpredictable variation in food include gathering information to reduce uncertainty (sampling) and strategically adjusting preference or aversion to variation in resources (variance-sensitivity). To manage the uncertainty of a novel cue, animals may generalize their previous experience with similar cues, or they may …

Examining The Effects Of Hyperglycemia On Retinal Regeneration, Emmanuella Ec Kyllians

Theses and Dissertations--Biology

Diabetes is a disease that affects how the body processes glucose, leading to a cascade of other complications, one of which is diabetic retinopathy (DR). DR is a neurovascular disease that affects the retina and research has revealed the role of retinal neurodegeneration in its development. Animal models like zebrafish have emerged as important tools for studying the molecular and cellular mechanisms underlying DR. On the other hand, retinitis pigmentosa (RP) is a degenerative disease that involves the progressive degeneration of rods and cones, and hyperglycemia has been found to impair regeneration. Therefore, this study aims to examine the effects …

Competition And Herbivory Influence The Survival, Growth, And Physiology Of Native Tree Seedlings In The Kentucky Inner Bluegrass Savanna-Woodland, James D. Shaffer

Theses and Dissertations--Biology

Terrestrial plant communities are shaped by competition for resources, herbivory, and abiotic processes. Savanna systems represent a dynamic coexistence of contrasting life forms (grasses and trees) shaped by competition and disturbance. The Kentucky Inner Bluegrass Savanna-Woodland (KIBSW) is described as an open woodland of shade intolerant species; however, climatic, and edaphic conditions can support closed-canopy forest. After European pioneer settlement (c1750-1800), over 99% of “savanna-woodlands” have been lost. KIBSW remnants are experiencing a recruitment failure, leading to a dominance shift in tree communities. I researched how tree-grass competition and mammalian herbivory influence KIBSW regeneration and maintenance. The KIBSW does not …

Parental Effects On Offspring Reaction Norms: Consequences For Complex Phenotypes In Variable Environments, Alexandra G. Cones

Theses and Dissertations--Biology

Organismal traits all exhibit some degree of environmental sensitivity, and both the strength and direction of these phenotypically plastic responses to the environment can evolve in adaptive ways. For example, parents can use information about their own environment to precondition the traits of their offspring so that they thrive in their future environment. This transgenerational plasticity can also alter the plasticity of offspring, but explicit investigations of this specific phenomenon are rare. I begin with a review of the literature and provide a quantitative genetic framework to investigate this phenomenon, which I then explore empirically using avian embryos. The metabolic …

Multilevel Phenotypic Integration Of Metabolism And Behavior In House Sparrows And Mice, Tim Salzman

Theses and Dissertations--Biology

Patterns of multilevel variation in behavior, both within and among individuals, raise challenging questions about underlying mechanisms and the selective pressures acting on them. One intriguing hypothesis is that physiology shows parallel multilevel variation, and so might represent a latent trait that integrates multilevel behavioral responses. For example, foraging acquires the fuel needed to maintain metabolism, and in turn, an individual’s metabolism affects expression of foraging, and other, behaviors. Metabolism and behavior thus might coevolve to become integrated traits. Despite the appeal of this hypothesis, numerous investigations into the link between metabolism and behavior have yielded largely equivocal results.

To …

Brain Barriers Virtual: An Interim Solution Or Future Opportunity?, Brianna M. Holder, Shaina E. Tolan, Kaleb K. Heinrich, Kaitlin C. Miller, Natalie Hudson, Geetika Nehra, Michelle E. Pizzo, Steffen E. Storck, William F. Elmquist, Britta Engelhardt, Irena Loryan, Michal Toborek, Bjoern Bauer, Anika M. S. Hartz, Brandon J. Kim

Biology Faculty Publications

Background: Scientifc conferences are vital communication events for scientists in academia, industry, and government agencies. In the brain barriers research feld, several international conferences exist that allow researchers to present data, share knowledge, and discuss novel ideas and concepts. These meetings are critical platforms for researchers to connect and exchange breakthrough fndings on a regular basis. Due to the worldwide COVID-19 pandemic, all in-person meetings were canceled in 2020. In response, we launched the Brain Barriers Virtual 2020 (BBV2020) seminar series, the frst stand-in virtual event for the brain barriers feld, to ofer scientists a virtual platform to present …

Glia Excitation In The Cns Modulates Intact Behaviors And Sensory-Cns-Motor Circuitry, Shelby Mccubbin, Douglas A. Harrison, Robin L. Cooper

Biology Faculty Publications

Glial cells play a role in many important processes, though the mechanisms through which they affect neighboring cells are not fully known. Insights may be gained by selectively activating glial cell populations in intact organisms utilizing the activatable channel proteins channel rhodopsin (ChR2XXL) and TRPA1. Here, the impacts of the glial-specific expression of these channels were examined in both larval and adult Drosophila. The Glia > ChR2XXL adults and larvae became immobile when exposed to blue light and TRPA1-expressed Drosophila upon heat exposure. The chloride pump expression in glia > eNpHR animals showed no observable differences in adults or larvae. In …